Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array

Bioinformatics

Volumn 27, Issue 3, 2011, Pages 303-310

  Gidskehaug, Lars ^a   Kent, Matthew ^a   Hayes, Ben J ^b   Lien, Sigbjørn ^a  

^a NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

^b Melbourne Collaborative Cohort Study (MCCS)   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

SALMO SALAR; SALMONIDAE;

ANIMAL; ARTICLE; ATLANTIC SALMON; CHROMOSOME MAP; COMPUTER PROGRAM; DNA MICROARRAY; GENETICS; GENOME; GENOTYPE; METHODOLOGY; NORWAY; REPRODUCIBILITY; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; CHROMOSOME MAPPING; GENOME; GENOTYPE; NORWAY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; SALMO SALAR; SOFTWARE;

EID: 79551599953     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq673     Document Type: Article

References (22)

1. Danzmann,R.G. et al. (2005) A comparative analysis of the rainbow trout genome with 2 other species of fish (Arctic charr and Atlantic salmon) within the tetraploid derivative Salmonidae family (subfamily: Salmoninae). Genome, 48, 1037-1051.
2. Danzmann,R.G. et al. (2008) Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (Rainbow trout and Atlantic salmon). BMC Genomics, 9, 557.
3. Dunning,M.J. et al. (2007) beadarray: R classes and methods for Illumina bead-based data. Bioinformatics, 23, 2183-2184.
4. Fredman,D. et al. (2004) Complex SNP-related sequence variation in segmental genome duplications. Nat. Genet., 36, 861-866.
5. Gentleman,R. et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol., 5, R80.
6. Gidskehaug,L. et al. (2007) A framework for significance analysis of gene expression data using dimension reduction methods. BMC Bioinformatics, 8, 346.
7. Green,P. et al. (1990) Documentation for CRI-MAP, Version 2.4.Washington University School of Medicine, St Louis, MO, USA.
8. Kent,M.P. et al. (2009) Development of 16.5 K SNP chip for Atlantic Salmon, Proceedings of the 17th Plant and Animal Genome Conference, January 10-14, 2009 San Diego, CA. http://www.intl-pag.org/
9. Macgregor,S. et al. (2008) Highly cost-efficient genome-wide association studies using DNA pools and dense SNP arrays. Nucleic Acids Res., 36, e35.
10. Meuwissen,T.H.E. et al. (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics, 157, 1819-1829.
11. Moen,T. et al. (2008) A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers. BMC Genomics, 9, 223.
12. Oosting,J. et al. (2007) High-resolution copy number analysis of paraffin-embedded archival tissue using SNP BeadArrays. Genome Res., 17, 368-376.
13. Peiffer,D. et al. (2006) High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Res., 16, 1136-1148.
14. Phillips,R.B. et al. (2009) Assignment of Atlantic salmon (Salmo salar) linkage groups to specific chromosomes: conservation of large syntenic blocks corresponding to whole chromosome arms in rainbow trout (Oncorhynchus mykiss). BMC Genetics, 10, 46.
15. Ritchie,M.E. et al. (2009) R/Bioconductor software for Illumina's Infinium wholegenome genotyping BeadChips. Bioinformatics, 25, 2621-2623.
16. Sánchez,C.C. et al. (2009) Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library. BMC Genomics, 10, 559.
17. Sémon,M. and Wolfe,K.H. (2007) Consequences of genome duplication. Curr. Opin. Genet. Dev., 17, 505-512.
18. Shen,R. et al. (2005) High-throughput SNP genotyping on universal bead arrays. Mutat. Res., 573, 70-82.
19. Smyth,G. and Speed,T. (2003) Normalization of cDNA microarray data. Methods, 31, 265-273.
20. Steemers,F.J. and Gunderson,K.L. (2007) Whole genome genotyping technologies on the BeadArray™ platform. Biotechnol. J., 2, 41-49.
21. Staaf,J. et al. (2008) Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios. BMC Bioinformatics, 9, 409.
22. Wolfe,K.H. (2001) Yesterday's polyploids and the mystery of diploidization. Nat. Rev. Genet., 2, 333-341.